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CPTAC has been conducted in multiple phases. For their the phase 3 prospective data collection activities TCIA has partnered with CPTAC to host both the radiology and pathology imaging data generated by the project. The other data types will be hosted in separate databases managed by the CPTAC program. TCIA will provide links to these resources as they become publicly available. You can join the CPTAC Imaging Special Interest Group to be notified of webinars & data releases, collaborate on common data wrangling tasks and seek out partners to explore research hypotheses!
CPTAC Phase 3 Histopathology and Radiology Imaging
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Imaging
Histopathology imaging and select pathology report details from approved CPTAC cases will be made available on TCIA at: https://cancerimagingarchive.net/datascope/cptac/.
A tutorial walk-through of the histopathology review system is available here.
Radiology Imaging
TCIA is also in the process of collecting radiology imaging from contracted CPTAC tissue sources sites. The imaging data will be made available on a quarterly release schedule. Data currently available includes:
Collection | Cancer Type | Location | Radiology Modalities | Radiology (Subjects |
) | Pathology (Subjects) | ||||
| CPTAC-AML | Acute Myeloid Leukemia | Bone Marrow | -- | -- | 38 |
Clear Cell Carcinoma | Kidney | CT |
| 222 | |||
Cutaneous Melanoma | Skin | MR, CT, CR |
| 73 | |||
Glioblastoma Multiforme | Brain | CT, MR |
| 120 | |||
| CPTAC-HNSCC | Head and Neck Squamous Cell Carcinoma | Head-Neck | CT, SC |
| 29 |
| 110 | |||
Squamous Cell Carcinoma | Lung | CR, CT, DX, PT |
| 114 | |||
Adenocarcinoma | Lung | CT, MR, PT, CR |
| 165 | |||
Ductal Adenocarcinoma | Pancreas | CT, MR, DX, CR |
43
| 85 | |||||
| CPTAC-SAR | Sarcomas | Soft Tissue | CT,MR | 3 | 71 |
Corpus Endometrial Carcinoma | Uterus | CT, MR, PT, CR |
33
| 181 |
Quick introduction to the TCIA CPTAC Pathology Portal:
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CPTAC Phase 2 - TCGA Cancer Proteome Studies
TCIA did not formally participate in CPTAC phase 2, but a small subset of the radiology imaging studies for this cohort are available due to overlap with NIH's Cancer Genome Atlas activity. Specifically there are 28 ovarian (TCGA-OV) and 14 breast (TCGA-BRCA) cases in TCIA which have corresponding CPTAC phase 2 proteomic analysis data. The Proteomic Analysis Data is available at: https://cptac-data-portal.georgetown.edu/cptacPublic/.
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Images and Clinical Data Downloads
These subsets of radiology images have been saved as Shared Lists can be accessed using the following nameslinks:
The clinical data for these subjects can be found in these spreadsheets:
References
An early CPTAC publication which reports on a more comprehensive collection of cases from those TCGA tumor data collections (BRCA and OV) can be found at: “Comprehensive quantitative analysis of ovarian and breast cancer tumor peptidomes”. Xu Z, et al., J Proteome Res. 2015 Jan 2;14(1):422-33. doi: 10.1021/pr500840w.
An excellent review of proteomic biomarkers is the publication: "Proteomics in cancer biomarkers discovery: challenges and applications." Sallam RM1. Dis Markers. 2015;2015:321370. doi: 10.1155/2015/321370.
Also: Identification of protein biomarkers in human serum using iTRAQ and shotgun mass spectrometry Methods Mol Biol. 2013;1061:291-307. doi: 10.1007/978-1-62703-589-7_18. Koutroukides TA1